Investigations of metabolic pathways cover a broad range of laboratory techniques. Lead drug substances are administered to different animals, humans, cell tissues and the like. The chemical metabolizing and physical pathways of detoxification or excretion of the drug in the organisms are observed by analyzing different types of samples (urine, plasma, tissues extractions). It is also common that the active substance is a metabolite of the administered drug. The samples are primarily analyzed by High Performance Liquid Chromatography-Mass Spectrometry systems dividing and purifying the sample fractions and providing information about the number and type of metabolites. Due to a lack of direct information about the molecular structure the metabolites are primarily characterized by mass differences and major ions, both derived from mass spectra. Since e.g. hydroxylation of a xenobiotic is a common starter for a detoxification process a mass difference of “+16” for example is likely to be assumed as an “—OH” added to the molecule, although the position of the group is not known at an early stage of a study. The drug under investigation can also be administered in a radio labeled form making the identification among similar organism immanent substances easier. For more detailed information about the molecule structures NMR measurements are performed. For localization of metabolites within organisms/organs also immuno staining techniques in tissue slices are used. The goal of such investigations is also to propose a pathway within the different organisms/conditions.
In order to gain insights into metabolic pathways means are important that allow the management and interpretation of the acquired genomic data. With the emergence of potentially very large datasets from high-throughput gene expression and proteomics experiments, there is a recognized need to relate such data to known networks of biochemical processes and interactions. In support of these activities, a well structured, yet flexible, system and method for managing and analyzing metabolic pathway data are required.